I have analyzed chip-seq raw data for two TFs oct4 and Nanog. i have a list of the enriched binding sites with their genomic coordinates and also using GREAT i have the gees that fall in these regions along with its TSS coordinates. Please suggest how do i correlate the binding sites of the two transcription factors???
you have a peak set of OCT4 and a peak set of Nanog. You can use bedtools intersect to find the how many sites are overlapping each other. If you want a correlation, you may creat a matrix below (1 means the peak is present, 0 means the peak is absent)
OCT4 Nanog peak1 1 1 peak2 0 1 peak3 1 0 peak4 1 1 ........
Then calculate the pearson correlation http://stats.stackexchange.com/questions/103801/is-it-meaningful-to-calculate-pearson-or-spearman-correlation-between-two-boolea or use other distance measurement.